Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma.
Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma.
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DOI：
10.1038/modpathol.2015.82
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发表时间：
2015-09
期刊：
影响因子：
--
通讯作者：
Barr FG
中科院分区：
文献类型：
--
作者：
Sun W;Chatterjee B;Wang Y;Stevenson HS;Edelman DC;Meltzer PS;Barr FG
横纹肌肉瘤包括两种主要亚型：融合阳性（PAX3-FOXO1 或 PAX7-FOXO1）和融合阴性。为了研究 DNA 甲基化在这些亚型中的重要性，我们分析了 37 种横纹肌肉瘤肿瘤和 10 种横纹肌肉瘤细胞系以及 8 种正常组织的甲基化谱。 DNA 甲基化的无监督聚类清楚地区分了融合阳性和融合阴性子集。与融合阴性肿瘤相比，融合阳性肿瘤的甲基化总体水平显着降低。与正常骨骼肌和骨髓的甲基化模式比较表明，融合阴性横纹肌肉瘤比融合阳性横纹肌肉瘤与这些正常组织更相似，并表明这些亚型之间的许多甲基化差异源于融合阳性横纹肌肉瘤中“异常”的高甲基化和低甲基化事件。综合甲基化和基因表达分析表明，融合阳性和融合阴性肿瘤之间的甲基化差异可能与 mRNA 表达呈正相关或负相关。有和没有差异甲基化的基因之间PAX3-FOXO1结合位点的分布没有显着差异。然而，PAX3-FOXO1 结合位点在差异甲基化和差异表达的基因中富集的发现表明，融合蛋白与 DNA 甲基化相互作用以调节靶基因表达。建立了 11 基因 DNA 甲基化特征，将横纹肌肉瘤肿瘤分为融合阳性和融合阴性子集，并通过焦磷酸测序测定进行验证。值得注意的是，与融合阴性肿瘤相比，EMILIN1（11基因特征的一部分）在融合阳性肿瘤中表现出更高的甲基化和更低的mRNA表达，并且在用5-aza-2'-脱氧胞苷处理后在多个融合阳性细胞系中表现出去甲基化和重新表达。总之，我们的研究表明，融合阳性和融合阴性横纹肌肉瘤肿瘤具有特征性甲基化谱，导致这些融合亚型之间的表达差异。这些发现表明横纹肌肉瘤中融合状态与表观遗传变化之间的重要关系，提出了一种确定融合状态的新方法，并可能确定横纹肌肉瘤的新治疗靶点。
Rhabdomyosarcoma comprises two major subtypes, fusion-positive (PAX3-FOXO1 or PAX7-FOXO1) and fusion-negative. To investigate the significance of DNA methylation in these subtypes, we analyzed methylation profiles of 37 rhabdomyosarcoma tumors and 10 rhabdomyosarcoma cell lines as well as 8 normal tissues. Unsupervised clustering of DNA methylation clearly distinguished the fusion-positive and fusion-negative subsets. The fusion-positive tumors showed substantially lower overall levels of methylation compared to fusion-negative tumors. Comparison to the methylation pattern of normal skeletal muscle and bone marrow indicates that fusion-negative rhabdomyosarcoma is more similar to these normal tissues than fusion-positive rhabdomyosarcoma, and suggests that many of the methylation differences between these subtypes arise from “aberrant” hyper- and hypomethylation events in fusion-positive rhabdomyosarcoma. Integrative methylation and gene expression analysis revealed that methylation differences between fusion-positive and fusion-negative tumors could either be positively or negatively associated with mRNA expression. There was no significant difference in the distribution of PAX3-FOXO1 binding sites between genes with and without differential methylation. However, the finding that PAX3-FOXO1 binding sites were enriched among genes that were both differentially methylated and differentially expressed suggests that the fusion protein interacts with DNA methylation to regulate target gene expression. An 11-gene DNA methylation signature, classifying the rhabdomyosarcoma tumors into fusion-positive and fusion-negative subsets, was established and validated by pyrosequencing assays. Notably, EMILIN1 (part of the 11-gene signature) showed higher methylation and lower mRNA expression in fusion-positive compared fusion-negative tumors, and demonstrated demethylation and re-expression in multiple fusion-positive cell lines after treatment with 5-aza-2’-deoxycytidine. In conclusion, our study demonstrates that fusion-positive and fusion-negative rhabdomyosarcoma tumors possess characteristic methylation profiles that contribute to the expression differences between these fusion subtypes. These findings indicate an important relationship between fusion status and epigenetic changes in rhabdomyosarcoma, present a novel approach for ascertaining fusion status, and may identify new therapeutic targets in rhabdomyosarcoma.
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影响因子：
5.3
作者：
Danussi, Carla;Belluz, Lisa Del Bel;Spessotto, Paola
通讯作者：
Spessotto, Paola
影响因子：
17.1
作者：
Aryee MJ;Liu W;Engelmann JC;Nuhn P;Gurel M;Haffner MC;Esopi D;Irizarry RA;Getzenberg RH;Nelson WG;Luo J;Xu J;Isaacs WB;Bova GS;Yegnasubramanian S
通讯作者：
Yegnasubramanian S
影响因子：
11.2
作者：
Cao, Liang;Yu, Yunkai;Meltzer, Paul S.
通讯作者：
Meltzer, Paul S.
影响因子：
4.1
作者：
Barr, FG;Smith, LM;Breitfeld, PP
通讯作者：
Breitfeld, PP
影响因子：
7.3
作者：
Lae, M.;Ahn, E. H.;Ladanyi, M.
通讯作者：
Ladanyi, M.